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// $Id$
//
// Copyright (C) 2005-2008 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#define PY_ARRAY_UNIQUE_SYMBOL rdmoltransforms_array_API
#include <RDBoost/python.h>
#include <RDBoost/import_array.h>
#include "numpy/arrayobject.h"
#include <GraphMol/ROMol.h>
#include <RDBoost/Wrap.h>
#include <GraphMol/Conformer.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <Geometry/Transform3D.h>
#include <Geometry/point.h>
namespace python = boost::python;
namespace RDKit {
PyObject *computeCanonTrans(const Conformer &conf,
const RDGeom::Point3D *center = 0,
bool normalizeCovar = false, bool ignoreHs = true) {
RDGeom::Transform3D *trans;
trans = MolTransforms::computeCanonicalTransform(conf, center, normalizeCovar,
ignoreHs);
npy_intp dims[2];
dims[0] = 4;
dims[1] = 4;
PyArrayObject *res = (PyArrayObject *)PyArray_SimpleNew(2, dims, NPY_DOUBLE);
double *resData = reinterpret_cast<double *>(PyArray_DATA(res));
const double *tdata = trans->getData();
memcpy(static_cast<void *>(resData), static_cast<const void *>(tdata),
4 * 4 * sizeof(double));
delete trans;
return PyArray_Return(res);
}
void transConformer(Conformer &conf, python::object trans) {
PyObject *transObj = trans.ptr();
if (!PyArray_Check(transObj)) {
throw_value_error("Expecting a numeric array for transformation");
}
PyArrayObject *transMat = reinterpret_cast<PyArrayObject *>(transObj);
unsigned int nrows = PyArray_DIM(transMat, 0);
unsigned int dSize = nrows * nrows;
double *inData = reinterpret_cast<double *>(PyArray_DATA(transMat));
RDGeom::Transform3D transform;
double *tData = transform.getData();
memcpy(static_cast<void *>(tData), static_cast<void *>(inData),
dSize * sizeof(double));
MolTransforms::transformConformer(conf, transform);
}
}
BOOST_PYTHON_MODULE(rdMolTransforms) {
python::scope().attr("__doc__") =
"Module containing functions to perform 3D operations like rotate and "
"translate conformations";
rdkit_import_array();
std::string docString =
"Compute the centroid of the conformation - hydrogens are ignored and no attention\n\
if paid to the difference in sizes of the heavy atoms\n";
python::def("ComputeCentroid", MolTransforms::computeCentroid,
(python::arg("conf"), python::arg("ignoreHs") = true),
docString.c_str());
docString =
"Compute the transformation required aligna conformer so that\n\
the the principal axes align up with the x,y, z axes\n\
The conformer itself is left unchanged\n\
ARGUMENTS:\n\
- conf : the conformer of interest\n\
- center : optional center point to compute the principal axes around (defaults to the centroid)\n\
- normalizeCovar : optionally normalize the covariance matrix by the number of atoms\n";
python::def(
"ComputeCanonicalTransform", RDKit::computeCanonTrans,
(python::arg("conf"), python::arg("center") = (RDGeom::Point3D *)(0),
python::arg("normalizeCovar") = false, python::arg("ignoreHs") = true),
docString.c_str());
python::def("TransformConformer", RDKit::transConformer,
"Transform the coordinates of a conformer");
docString =
"Canonicalize the orientation of a conformer so that its principal axes\n\
around the specified center point coincide with the x, y, z axes\n\
\n\
ARGUMENTS:\n\
- conf : conformer of interest \n\
- center : optionally center point about which the principal axes are computed \n\
if not specified the centroid of the conformer will be used\n\
- normalizeCovar : Optionally normalize the covariance matrix by the number of atoms\n";
python::def(
"CanonicalizeConformer", MolTransforms::canonicalizeConformer,
(python::arg("conf"), python::arg("center") = (RDGeom::Point3D *)(0),
python::arg("normalizeCovar") = false, python::arg("ignoreHs") = true),
docString.c_str());
python::def("CanonicalizeMol", MolTransforms::canonicalizeMol,
(python::arg("mol"), python::arg("normalizeCovar") = false,
python::arg("ignoreHs") = true),
"Loop over the conformers in a molecule and canonicalize their "
"orientation");
python::def(
"GetBondLength", &MolTransforms::getBondLength,
(python::arg("conf"), python::arg("iAtomId"), python::arg("jAtomId")),
"Returns the bond length in angstrom between atoms i, j\n");
python::def("SetBondLength", &MolTransforms::setBondLength,
(python::arg("conf"), python::arg("iAtomId"),
python::arg("jAtomId"), python::arg("value")),
"Sets the bond length in angstrom between atoms i, j; "
"all atoms bonded to atom j are moved\n");
python::def("GetAngleRad", &MolTransforms::getAngleRad,
(python::arg("conf"), python::arg("iAtomId"),
python::arg("jAtomId"), python::arg("kAtomId")),
"Returns the angle in radians between atoms i, j, k\n");
python::def("GetAngleDeg", &MolTransforms::getAngleDeg,
(python::arg("conf"), python::arg("iAtomId"),
python::arg("jAtomId"), python::arg("kAtomId")),
"Returns the angle in degrees between atoms i, j, k\n");
python::def(
"SetAngleRad", &MolTransforms::setAngleRad,
(python::arg("conf"), python::arg("iAtomId"), python::arg("jAtomId"),
python::arg("kAtomId"), python::arg("value")),
"Sets the angle in radians between atoms i, j, k; "
"all atoms bonded to atom k are moved\n");
python::def(
"SetAngleDeg", &MolTransforms::setAngleDeg,
(python::arg("conf"), python::arg("iAtomId"), python::arg("jAtomId"),
python::arg("kAtomId"), python::arg("value")),
"Sets the angle in degrees between atoms i, j, k; "
"all atoms bonded to atom k are moved\n");
python::def(
"GetDihedralRad", &MolTransforms::getDihedralRad,
(python::arg("conf"), python::arg("iAtomId"), python::arg("jAtomId"),
python::arg("kAtomId"), python::arg("lAtomId")),
"Returns the dihedral angle in radians between atoms i, j, k, l\n");
python::def(
"GetDihedralDeg", &MolTransforms::getDihedralDeg,
(python::arg("conf"), python::arg("iAtomId"), python::arg("jAtomId"),
python::arg("kAtomId"), python::arg("lAtomId")),
"Returns the dihedral angle in degrees between atoms i, j, k, l\n");
python::def(
"SetDihedralRad", &MolTransforms::setDihedralRad,
(python::arg("conf"), python::arg("iAtomId"), python::arg("jAtomId"),
python::arg("kAtomId"), python::arg("lAtomId"), python::arg("value")),
"Sets the dihedral angle in radians between atoms i, j, k, l; "
"all atoms bonded to atom l are moved\n");
python::def("SetDihedralDeg", &MolTransforms::setDihedralDeg,
"Sets the dihedral angle in degrees between atoms i, j, k, l; "
"all atoms bonded to atom l are moved\n");
}
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